Commit a32bc102 authored by Peter van 't Hof's avatar Peter van 't Hof

Fix ode style

parent 782140f5
......@@ -136,12 +136,12 @@ object VcfStats extends ToolCommand {
generalWiggle: List[String] = Nil,
genotypeWiggle: List[String] = Nil) extends AbstractArgs
private val generalWiggleOptions = List("Total","Biallelic", "ComplexIndel", "Filtered", "FullyDecoded", "Indel", "Mixed",
private val generalWiggleOptions = List("Total", "Biallelic", "ComplexIndel", "Filtered", "FullyDecoded", "Indel", "Mixed",
"MNP", "MonomorphicInSamples", "NotFiltered", "PointEvent", "PolymorphicInSamples",
"SimpleDeletion", "SimpleInsertion", "SNP", "StructuralIndel", "Symbolic",
"SymbolicOrSV", "Variant")
private val genotypeWiggleOptions = List("Total", "Het", "HetNonRef", "Hom", "HomRef", "HomVar", "Mixed", "NoCall", "NonInformative",
private val genotypeWiggleOptions = List("Total", "Het", "HetNonRef", "Hom", "HomRef", "HomVar", "Mixed", "NoCall", "NonInformative",
"Available", "Called", "Filtered", "Variant")
/** Parsing commandline arguments */
......@@ -185,8 +185,8 @@ object VcfStats extends ToolCommand {
opt[String]("generalWiggle") unbounded () action { (x, c) =>
c.copy(generalWiggle = x :: c.generalWiggle, writeBinStats = true)
} validate {
x => if (generalWiggleOptions.contains(x)) success else failure (s"""Nonexistent field $x""")
}text
x => if (generalWiggleOptions.contains(x)) success else failure(s"""Nonexistent field $x""")
} text
"""
|Create a wiggle track with bin size <binSize> for any of the following statistics:
|Total
......
......@@ -16,7 +16,7 @@
package nl.lumc.sasc.biopet.tools
import java.io.File
import java.nio.file.{Files, Paths}
import java.nio.file.{ Files, Paths }
import htsjdk.variant.variantcontext.Allele
import htsjdk.variant.vcf.VCFFileReader
......@@ -37,7 +37,6 @@ class VcfStatsTest extends TestNGSuite with Matchers {
Paths.get(getClass.getResource(p).toURI).toString
}
@Test
def testSampleToSampleStats(): Unit = {
val s1 = SampleToSampleStats()
......@@ -127,62 +126,62 @@ class VcfStatsTest extends TestNGSuite with Matchers {
@Test
def testMergeStatsMap = {
val m1 : mutable.Map[Any, Int] = mutable.Map("a" -> 1)
val m2 : mutable.Map[Any, Int] = mutable.Map("b" -> 2)
val m1: mutable.Map[Any, Int] = mutable.Map("a" -> 1)
val m2: mutable.Map[Any, Int] = mutable.Map("b" -> 2)
mergeStatsMap(m1, m2)
m1 should equal (mutable.Map("a" -> 1, "b" -> 2))
m1 should equal(mutable.Map("a" -> 1, "b" -> 2))
val m3 : mutable.Map[Any, Int] = mutable.Map(1 -> 500)
val m4 : mutable.Map[Any, Int] = mutable.Map(6 -> 125)
val m3: mutable.Map[Any, Int] = mutable.Map(1 -> 500)
val m4: mutable.Map[Any, Int] = mutable.Map(6 -> 125)
mergeStatsMap(m3, m4)
m3 should equal (mutable.Map(1 -> 500, 6 -> 125))
m3 should equal(mutable.Map(1 -> 500, 6 -> 125))
mergeStatsMap(m1, m3)
m1 should equal (mutable.Map("a" -> 1, "b" -> 2, 1 -> 500, 6 -> 125))
m1 should equal(mutable.Map("a" -> 1, "b" -> 2, 1 -> 500, 6 -> 125))
}
@Test
def testMergeNestedStatsMap = {
val m1 : mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map("test" ->
val m1: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map("test" ->
mutable.Map("nested" -> mutable.Map("a" -> 1)))
val m2: Map[String, Map[String, Map[Any, Int]]] = Map("test" ->
Map("nested" -> Map("b" -> 2)))
mergeNestedStatsMap(m1, m2)
m1 should equal (mutable.Map("test" -> mutable.Map("nested" -> mutable.Map("a" -> 1, "b" -> 2))))
m1 should equal(mutable.Map("test" -> mutable.Map("nested" -> mutable.Map("a" -> 1, "b" -> 2))))
val m3 : mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map("test" ->
val m3: mutable.Map[String, mutable.Map[String, mutable.Map[Any, Int]]] = mutable.Map("test" ->
mutable.Map("nestedd" -> mutable.Map(1 -> 500)))
val m4: Map[String, Map[String, Map[Any, Int]]] = Map("test" ->
Map("nestedd" -> Map(6 -> 125)))
mergeNestedStatsMap(m3, m4)
m3 should equal (mutable.Map("test" -> mutable.Map("nestedd" -> mutable.Map(1 -> 500, 6 -> 125))))
m3 should equal(mutable.Map("test" -> mutable.Map("nestedd" -> mutable.Map(1 -> 500, 6 -> 125))))
val m5 = m3.toMap.map(x => x._1 -> x._2.toMap.map(y => y._1 -> y._2.toMap))
mergeNestedStatsMap(m1, m5)
m1 should equal (mutable.Map("test" -> mutable.Map("nested" -> mutable.Map("a" -> 1, "b" -> 2),
"nestedd" -> mutable.Map(1 -> 500, 6 -> 125))))
m1 should equal(mutable.Map("test" -> mutable.Map("nested" -> mutable.Map("a" -> 1, "b" -> 2),
"nestedd" -> mutable.Map(1 -> 500, 6 -> 125))))
}
@Test
def testValueOfTsv = {
val i = new File(resourcePath("/sample.tsv"))
valueFromTsv(i, "Sample_ID_1", "library") should be (Some("Lib_ID_1"))
valueFromTsv(i, "Sample_ID_2", "library") should be (Some("Lib_ID_2"))
valueFromTsv(i, "Sample_ID_1", "bam") should be (Some("MyFirst.bam"))
valueFromTsv(i, "Sample_ID_2", "bam") should be (Some("MySecond.bam"))
valueFromTsv(i, "Sample_ID_3", "bam") should be (empty)
valueFromTsv(i, "Sample_ID_1", "library") should be(Some("Lib_ID_1"))
valueFromTsv(i, "Sample_ID_2", "library") should be(Some("Lib_ID_2"))
valueFromTsv(i, "Sample_ID_1", "bam") should be(Some("MyFirst.bam"))
valueFromTsv(i, "Sample_ID_2", "bam") should be(Some("MySecond.bam"))
valueFromTsv(i, "Sample_ID_3", "bam") should be(empty)
}
@Test
......@@ -224,7 +223,6 @@ class VcfStatsTest extends TestNGSuite with Matchers {
"--generalWiggle", x))
)
// returns null when validation fails
def validateArgs(array: Array[String]): Option[Args] = {
val argsParser = new OptParser
......@@ -249,7 +247,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
val one: Any = 1
val two: Any = 2
val text: Any = "hello"
val text2 : Any = "goodbye"
val text2: Any = "goodbye"
sortAnyAny(one, two) shouldBe true
sortAnyAny(two, one) shouldBe false
......@@ -306,7 +304,6 @@ class VcfStatsTest extends TestNGSuite with Matchers {
general.get("Symbolic") shouldEqual Some(0)
general.get("SimpleInsertion") shouldEqual Some(1)
val total = blah.get("total").get
total.get("SampleDistribution-NonInformative") shouldEqual Some(Map(0 -> 1))
total.get("SampleDistribution-Called") shouldEqual Some(Map(3 -> 1))
......@@ -353,10 +350,10 @@ class VcfStatsTest extends TestNGSuite with Matchers {
val genotype = record.getGenotype(0)
val blah = checkGenotype(record, genotype, List())
blah.get("chrQ") should not be empty
blah.get("total") should not be empty
val chrq = blah.get("chrQ").get
chrq.get("GQ") shouldEqual Some(Map(99 -> 1))
chrq.get("AD") shouldEqual Some(Map(24 -> 1, 21 -> 1))
......@@ -365,7 +362,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
chrq.get("AD-alt") shouldEqual Some(Map(21 -> 1))
chrq.get("AD-ref") shouldEqual Some(Map(24 -> 1))
chrq.get("general") should not be empty
val general = chrq.get("general").get
general.get("Hom") shouldEqual Some(0)
general.get("NoCall") shouldEqual Some(0)
......
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